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It would probably be of use to give which CAD system you use. There was a thread about a two layer board being interpreted as 4 layer and the admin had PM’ed the OP to share his files to be used in debug. I’m not sure how/if this was resolved.
I have never used panels or arrays with DKRed. I just use singles as Vscoring is not supported.
I work in Eagle7 and my only issue has been with the graphical representation of the excellon drill file. Number of decimal places not scaled properly. Looks wonky on screen but boards were perfect.
Additional info. I am using Altium 23.5.1. This board I ordered from another vendor with no issues raised and i received and assembled them with no problem. I wanted to order a new batch and wanted to see if digikey red would either be cheaper or faster.
As an independent Gerber review, I use GERBV. It also does not auto-scale my Eagle generated excellon drill file so I have to manually set number of places. http://gerbv.geda-project.org/